commit: dc849f2aa34abfd239c23d07515ff42917fd8552 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Wed Mar 8 21:35:39 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Wed Mar 8 22:16:21 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=dc849f2a
sci-biology/blat: Remove old Package-Manager: Portage-2.3.4, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4165 sci-biology/blat/blat-34-r1.ebuild | 44 ------- sci-biology/blat/blat-34.ebuild | 33 ----- sci-biology/blat/files/34-gentoo.patch | 226 --------------------------------- 3 files changed, 303 deletions(-) diff --git a/sci-biology/blat/blat-34-r1.ebuild b/sci-biology/blat/blat-34-r1.ebuild deleted file mode 100644 index 52079d22bea..00000000000 --- a/sci-biology/blat/blat-34-r1.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=4 - -inherit eutils toolchain-funcs - -MY_PN="${PN}Src" - -DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner" -HOMEPAGE="http://www.cse.ucsc.edu/~kent/"; -SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip"; - -SLOT="0" -LICENSE="blat" -KEYWORDS="~amd64 ~x86 ~x64-macos" -IUSE="" - -S="${WORKDIR}/${MY_PN}" - -DEPEND="app-arch/unzip" -RDEPEND="" - -src_prepare() { - epatch "${FILESDIR}"/${PV}-gentoo.patch - sed \ - -e "1i\CFLAGS=${CFLAGS}" \ - -e "1i\LDFLAGS=${LDFLAGS}" \ - -i inc/common.mk || die - tc-export CC -} - -src_compile() { - MACHTYPE=$(tc-arch) - [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" - mkdir -p "${S}/bin/${MACHTYPE}" - emake MACHTYPE="${MACHTYPE}" HOME="${S}" LDFLAGS="${LDFLAGS}" -} - -src_install() { - MACHTYPE=$(tc-arch) - [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" - dobin "${S}/bin/${MACHTYPE}/"* -} diff --git a/sci-biology/blat/blat-34.ebuild b/sci-biology/blat/blat-34.ebuild deleted file mode 100644 index 3ec0eb05bdb..00000000000 --- a/sci-biology/blat/blat-34.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -inherit toolchain-funcs - -DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner" -LICENSE="blat" -HOMEPAGE="http://www.cse.ucsc.edu/~kent/"; -SLOT="0" -IUSE="" -KEYWORDS="amd64 x86" - -MY_PN="${PN}Src" -SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip"; -S="${WORKDIR}/${MY_PN}" - -DEPEND="app-arch/unzip" -RDEPEND="" - -src_compile() { - MACHTYPE=$(tc-arch) - [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" - sed -i 's/-Werror//; s/CFLAGS=//;' "${S}/inc/common.mk" - sed -i 's/\(${STRIP} \)/#\1/' "${S}"/{*/makefile,utils/*/makefile,*/*.mk} - mkdir -p "${S}/bin/${MACHTYPE}" - emake MACHTYPE="${MACHTYPE}" HOME="${S}" || die "emake failed" -} - -src_install() { - MACHTYPE=$(tc-arch) - [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" - dobin "${S}/bin/${MACHTYPE}/"* -} diff --git a/sci-biology/blat/files/34-gentoo.patch b/sci-biology/blat/files/34-gentoo.patch deleted file mode 100644 index 8bdd05bff68..00000000000 --- a/sci-biology/blat/files/34-gentoo.patch +++ /dev/null @@ -1,226 +0,0 @@ - blat/makefile | 2 +- - gfClient/makefile | 2 +- - gfServer/makefile | 2 +- - hg/pslPretty/makefile | 2 +- - hg/pslReps/makefile | 2 +- - hg/pslSort/makefile | 2 +- - inc/common.mk | 11 +++-------- - makefile | 28 ++++++++++++++-------------- - utils/faToNib/makefile | 2 +- - utils/faToTwoBit/makefile | 2 +- - utils/nibFrag/makefile | 2 +- - utils/twoBitInfo/makefile | 2 +- - utils/twoBitToFa/makefile | 2 +- - 13 files changed, 28 insertions(+), 33 deletions(-) - -diff --git a/blat/makefile b/blat/makefile -index b889c7b..739503a 100644 ---- a/blat/makefile -+++ b/blat/makefile -@@ -7,7 +7,7 @@ MYLIBS = $(MYLIBDIR)/jkOwnLib.a $(MYLIBDIR)/jkweb.a - O = blat.o - - blat: $O $(MYLIBS) -- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L - ${STRIP} ${BINDIR}/blat${EXE} - - all: -diff --git a/gfClient/makefile b/gfClient/makefile -index c3288de..36e957e 100644 ---- a/gfClient/makefile -+++ b/gfClient/makefile -@@ -8,5 +8,5 @@ O = gfClient.o - X = gfClient - - gfClient: $O $(MYLIBS) -- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L - ${STRIP} ${BINDIR}/$X${EXE} -diff --git a/gfServer/makefile b/gfServer/makefile -index c06b3a5..f042d22 100644 ---- a/gfServer/makefile -+++ b/gfServer/makefile -@@ -8,7 +8,7 @@ O = gfServer.o - X = gfServer - - gfServer: $O $(MYLIBS) -- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L - ${STRIP} ${BINDIR}/$X${EXE} - - test: -diff --git a/hg/pslPretty/makefile b/hg/pslPretty/makefile -index c780b96..cbbcd0d 100644 ---- a/hg/pslPretty/makefile -+++ b/hg/pslPretty/makefile -@@ -8,7 +8,7 @@ MYLIBS = $(MYLIBDIR)/jkweb.a - O = pslPretty.o - - pslPretty: $O $(MYLIBS) -- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L - - test:: testRna testDnax - -diff --git a/hg/pslReps/makefile b/hg/pslReps/makefile -index 6e8f6d7..2b73b60 100644 ---- a/hg/pslReps/makefile -+++ b/hg/pslReps/makefile -@@ -9,7 +9,7 @@ MYLIBS = $(MYLIBDIR)/jkweb.a - O = pslReps.o - - pslReps: $O $(MYLIBS) -- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L - - lib: - cd ../../lib && ${MAKE} -diff --git a/hg/pslSort/makefile b/hg/pslSort/makefile -index 81fe083..eb63257 100644 ---- a/hg/pslSort/makefile -+++ b/hg/pslSort/makefile -@@ -8,7 +8,7 @@ MYLIBS = $(MYLIBDIR)/jkweb.a - O = pslSort.o - - pslSort: $O $(MYLIBS) -- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L - - - lib: -diff --git a/inc/common.mk b/inc/common.mk -index 1823163..3a04e2b 100644 ---- a/inc/common.mk -+++ b/inc/common.mk -@@ -1,20 +1,15 @@ --CC=gcc --ifeq (${COPT},) -- COPT=-O --endif --CFLAGS= - HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} - HG_WARN=-Wformat -Wimplicit -Wuninitialized -Wreturn-type - HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc - - # Stronger warning checks, and warnings-->errors, for libraries and CGIs: - ifeq (darwin,$(findstring darwin,${OSTYPE})) -- HG_WARN_ERR = -DJK_WARN -Wall -Werror -Wno-unused-variable -+ HG_WARN_ERR = -DJK_WARN -Wall -Wno-unused-variable - else - ifeq (solaris,$(findstring solaris,${OSTYPE})) - HG_WARN_ERR = -DJK_WARN -Wall - else -- HG_WARN_ERR = -DJK_WARN -Wall -Werror -+ HG_WARN_ERR = -DJK_WARN -Wall - endif - endif - # Apply the stronger checks to all code on our development machine: -@@ -37,7 +32,7 @@ ifeq (${BINDIR},) - endif - MKDIR=mkdir -p - ifeq (${STRIP},) -- STRIP=strip -+ STRIP=true - endif - CVS=cvs - -diff --git a/makefile b/makefile -index 6f9fddf..dded1cd 100644 ---- a/makefile -+++ b/makefile -@@ -1,18 +1,18 @@ - all: -- cd lib && ${MAKE} -- cd jkOwnLib && ${MAKE} -- cd blat && $(MAKE) -- cd gfClient && $(MAKE) -- cd gfServer && $(MAKE) -- cd hg/pslPretty && $(MAKE) -- cd hg/pslReps && $(MAKE) -- cd hg/pslSort && $(MAKE) -- cd utils/nibFrag && $(MAKE) -- cd utils/faToNib && $(MAKE) -- cd utils/faToTwoBit && $(MAKE) -- cd utils/twoBitToFa && $(MAKE) -- cd utils/twoBitInfo && $(MAKE) -- cd webBlat && $(MAKE) -+ $(MAKE) -C lib -+ $(MAKE) -C jkOwnLib -+ $(MAKE) -C blat -+ $(MAKE) -C gfClient -+ $(MAKE) -C gfServer -+ $(MAKE) -C hg/pslPretty -+ $(MAKE) -C hg/pslReps -+ $(MAKE) -C hg/pslSort -+ $(MAKE) -C utils/nibFrag -+ $(MAKE) -C utils/faToNib -+ $(MAKE) -C utils/faToTwoBit -+ $(MAKE) -C utils/twoBitToFa -+ $(MAKE) -C utils/twoBitInfo -+ $(MAKE) -C webBlat - - clean: - rm -f */*.o */*/*.o -diff --git a/utils/faToNib/makefile b/utils/faToNib/makefile -index fd0e3eb..63a1593 100644 ---- a/utils/faToNib/makefile -+++ b/utils/faToNib/makefile -@@ -8,4 +8,4 @@ MYLIBS = $(MYLIBDIR)/jkweb.a - O = faToNib.o - - faToNib: $O $(MYLIBS) -- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L -diff --git a/utils/faToTwoBit/makefile b/utils/faToTwoBit/makefile -index b1b44a9..1e8c1c8 100644 ---- a/utils/faToTwoBit/makefile -+++ b/utils/faToTwoBit/makefile -@@ -7,7 +7,7 @@ MYLIBS = ${MYLIBDIR}/jkweb.a - O = faToTwoBit.o - - faToTwoBit: $O ${MYLIBS} -- ${CC} ${COPT} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L -+ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L - ${STRIP} ${BINDIR}/faToTwoBit${EXE} - - clean: -diff --git a/utils/nibFrag/makefile b/utils/nibFrag/makefile -index 260a6f3..e37b9ab 100755 ---- a/utils/nibFrag/makefile -+++ b/utils/nibFrag/makefile -@@ -4,7 +4,7 @@ include ../../inc/common.mk - O = nibFrag.o - - nibFrag: $(O) -- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a - - - -diff --git a/utils/twoBitInfo/makefile b/utils/twoBitInfo/makefile -index 649784f..9434d1c 100644 ---- a/utils/twoBitInfo/makefile -+++ b/utils/twoBitInfo/makefile -@@ -7,7 +7,7 @@ MYLIBS = ${MYLIBDIR}/jkweb.a - O = twoBitInfo.o - - twoBitInfo: $O ${MYLIBS} -- ${CC} ${COPT} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L -+ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L - ${STRIP} ${BINDIR}/twoBitInfo${EXE} - - clean: -diff --git a/utils/twoBitToFa/makefile b/utils/twoBitToFa/makefile -index cf979f2..081f3b8 100644 ---- a/utils/twoBitToFa/makefile -+++ b/utils/twoBitToFa/makefile -@@ -8,7 +8,7 @@ MYLIBS = ${MYLIBDIR}/jkweb.a - O = twoBitToFa.o - - twoBitToFa: $O ${MYLIBS} -- ${CC} ${COPT} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L -+ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L - #${STRIP} ${BINDIR}/twoBitToFa${EXE} - - clean:
